Fill in the blanks with the primary protein structure of the f...

Question

Fill in the blanks with the primary protein structure of the following peptide. Circle all the α-carbons.

Peptide structure showing amino acids; circle α-carbons for primary structure analysis.

The above peptide is an effective buffer at pH 10. Which amino acid residue is responsible for that?

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Accepted Answer

So this practice problem is broken up into 2 parts, part a and part b. And part a says to fill in the blanks with the primary protein structure, for the following peptide in the figure. And then it it also wants to circle all of the alpha carbons. And so, again, what we have over here on the far left are our mnemonics to help us memorize all 20 amino acids in the 4 groups that they fall under. So again, the first one that we have is GAV lymph for the non polar. The next is the, Fat Young Whipper Snappers for the aromatic ones. Then we have the polar amino acids, which is Santa's team crafts new quilts. And then, of course, last but not least are the charged amino acids, dragons eat knights riding horses. And so what we have over here on the far left of our peptide is our amino group. So here's our amino group and notice that it's bonded to an alpha carbon. Here's our alpha carbon right here. And so notice that it's an alpha carbon because we have an R group extending off of it. Here's our R group and notice that this R group has an aromatic benzene ring, so that means it's got to be one of our, aromatic amino acids here. And notice that it's basically, like phenylalanine, it's like alanine with a phenyl group. But notice that there's also this hydroxyl group baby that's coming off. So this must be our tyrosine because remember, tyrosine here is essentially phenylalanine with a hydroxyl group baby. So because this R group right here is tyrosine's R group, we'll go ahead and put tyrosine's 3 letter code in here. It's not specified for one letter code, so let's put tyrosine's 3 letter code. So t y r, that's tyrosine. So then, what we have is our our carbonyl group bonded to a nitrogen, so that must mean that this is our peptide bond. And then the next one is must be an alpha carbon. So here what we have is an alpha carbon. And notice that it's bonded to 2 hydrogens, which means that its r group is literally just a hydrogen. And so because its r group is a hydrogen, that must mean that this is glycine because remember, glycine's r group is literally so easy to remember that it's just it just glides right on through and it's just a hydrogen. So this, because this r group here is just a hydrogen atom, that must mean that our next amino acid is just glycine and its three letter code is just gl y. So then next, what we have is our carbonyl group and it's bonded to a nitrogen, so, of course, that must mean that this is our amide linkage in our second peptide bond. Then, notice the nitrogen is bonded to alpha carbon. And again, what we see is that our alpha carbon has 2 hydrogens coming off of it here, so that must mean that one of these is its r group. And because it has a hydrogen of an r group, again, it's gonna be our glycine, so we can put glycine in again. So we've got 2 back to back glycines. Then, what we have is another carbonyl group, and the carbonyl group is bounded to a nitrogen, so that must mean that we have another amide linkage right here, so that's our 3rd peptide bond. And the next one must be the alpha carbon. So here's our alpha carbon right here. And notice that this alpha carbon has bonded to an R group that is this guy right here. And notice that it has another benzene ring and this benzene ring must mean that it must be one of our aromatic amino acids and it's just alanine with a phenyl group. It's literally just alanine with a phenyl group, which means that it must be phenylalanine over here, which is f. And its three letter code for phenylalanine is just p h e. So then next, what we have is a carbonyl group. So we've got a carbonyl group right here bonded to a nitrogen, which must mean that this bond here must be our, amide linkage in our 4th peptide bond. And then next, what we have is our alpha carbon and our alpha carbon is bonded to an r group up here. And notice that this r group kinda looks like valine, right? It's got this v shape in here. You guys see that v shape? So it kinda looks like it's gonna be valine, which would be here. But notice that it's actually a little bit extended than valine. It's got it's kinda like a loose version of valine. So that must mean that this is actually leucine because remember leucine is just a loose extension of valine. So this is actually leucine's r group right here. And because it's leucine's r group, we can go ahead and put leucine's 3 letter code right here, which is just l e u. And then last, what we'll have is our free carboxyl group. So again, what we've done is we've revealed the primary sequence from the n terminal end to the c terminal end way over here. So that concludes the first part, part a. So now, in part b, it's asking us, the above peptide is an effective buffer at pH 10. So it's telling us that it is an effective buffer at pH 10. And it says, which amino acid residue is responsible for that? And so, what remember that, an effective buffer is essentially gonna have an ionizable group with a pKa that is, within that's very close to the pH that it's an effective buffer at. So the effective buffering range of an ionizable group is gonna be within plus or minus 1 of the pKa. And so we are looking for ionizable groups here, and so, remember, we're gonna need to recall our ionizable amino acids, and the mnemonic to help us memorize the ionizable amino acids is just yucky crazy dragons eat knights riding horses. And so what you'll notice is that none of these amino acids up here, so all of these that we identified, glycine, phenylalanine, and leucine, none of these are ionizable. None of them fall under here. And so because, none of them fall into our, ionizable amino acid group, then the only one that does is Tyrosine, which is over here. Tyrosine is represented by the y here in our, ionizable amino acids. That must mean that tyrosine is the only one that has an ionizable group and so that is, capable of being an effective buffer at pH 10. So the this ionizable group that's over here on the far left with this carboxyl group, that one's gonna have a p k around 2. So p k a is 2. And so because the p k a is 2, that's not close to pH of 10 at all. So we want it to be really close to 10. But over here with our, tyrosine residue, which would be this entire thing, we've got the amino group, which is this guy, which we now have a pKa in the ballpark of 9 to 10.5, which is a lot closer to 10 than the pKa of 2. And also, Tyrosine's, R group is also ionizable and it turns out that Tyrosine's, R group has a pKa right around 10 as well. So, basically, this entire residue, tyrosine, is responsible for, the above peptide being an effective buffer at pH 10. So So what we can do is put in tyrosine or we could just say the first residue. And so that answers this practice problem and I'll see you guys in our next one.

Struggling with Biochemistry?

Fill in the blanks with the primary protein structure of the following peptide. Circle all the α-carbons.

The above peptide is an effective buffer at pH 10. Which amino acid residue is responsible for that?
________________

Watch next

Primary Structure of Protein practice set

Struggling with Biochemistry?

Fill in the blanks with the primary protein structure of the following peptide. Circle all the α-carbons.The above peptide is an effective buffer at pH 10. Which amino acid residue is responsible for that?________________

Watch next

Primary Structure of Protein practice set

Fill in the blanks with the primary protein structure of the following peptide. Circle all the α-carbons.

The above peptide is an effective buffer at pH 10. Which amino acid residue is responsible for that?
________________